In the past decades the study of human evolution has been expanded significantly through the addition of several biomolecular approaches. The palaeoproteomic analysis of skeletal material has recently emerged as one such novel biomolecular approach, as proteins preserve over longer time periods in mineralised tissues compared to DNA. Ancient protein sequences have been found to be phylogenetically informative, even for hominin fossils. As a result, palaeoproteomic analysis can be applied to skeletal material across the Pleistocene and can provide complementary molecular evidence on hominin evolutionary relationships on a global scale.

Like other methods to study ancient evolutionary relationships among hominin fossils, the palaeoproteomic approach comes with its own set of challenges. Palaeoanthropological and archaeological remains are rare and finite, and contain relatively small proteomes. They contain proteins that have been fragmented into short peptides and amino acids that have been heavily modified. To address these challenges, and realise the full potential of the palaeoproteomic approach, further proteomic methods need to be developed and optimised, and understanding of the biology of skeletal proteomes needs to be increased.

The PROSPER project aims to address these challenges found in palaeoproteomics and human evolutionary research.

Skeletal proteome variation

Sample selection is an important and highly relevant part of any destructive analysis. To expand our knowledge of skeletal proteomes, PROSPER aims to study the variation in the hominin skeletal proteome between and within different skeletal elements. This knowledge will help guide sampling strategies and sample selection from highly precious archaeological material, causing minimal alterations of the material.

Enhanced extraction approaches to Pleistocene skeletal proteomes

The PROSPER project aims to develop laboratory methods that will maximise proteome size and coverage of phylogenetically relevant proteins. With increased knowledge of hominin skeletal proteome and more robust laboratory methods, PROSPER aims to maximise the amount of information that can be extracted with minimal damage to irreplaceable fossils.

Ancient hominin proteomes

The PROSPER project aims to study human evolution during the Middle and Late Pleistocene using phyloproteomic methods. The PROSPER project aims to analyze Middle and Late Pleistocene hominins that generally lack ancient DNA preservation, and sequence their proteomes using the improved sampling and extraction methods generated as part of the project. These proteomes will be highly informative to understand the emergence and distribution of archaic hominins as well as the association of particular hominin fossils to known (Neanderthals, Denisovans, modern humans) and unknown hominin lineages.

This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 948365).